GWAS summary file including risk allele, protective allele and disease

Question

[Shicheng Guo]

Hi All,

I hope to find a summary table including risk allele, protective allele and disease to summary the previous all GWAS studies. I download a summary file from GWAS catalog, however, this summary is not so good. No labelled risk allele and protective allele.

I think actually when the authors submit GWAS or association study, they should explicitly provide these information to database, right?

Thanks.

[Denise CS]

No, the authors not always provide this information to the journal or make it available through supplementary materials. I'd have thought that some of the info you are after is available Ensembl, known as "associated allele" in the "Phenotype data" table for a given rsID.

Answer 1

[btsui]

NCBI dbSNP provides an VCF (https://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/All_20180418.vcf.gz ) that summarizes each variant. For example, F7 bit 8 denote whether it is linked to the disease as shown in the following snapshot:

Full characteristics of dbSNP variant are listed here: https://ftp.ncbi.nlm.nih.gov/snp/specs/dbSNP_BitField_latest.pdf

I also have written some code on parsing and doing basic stats on the dbSNP VCF before: https://github.com/brianyiktaktsui/Skymap/blob/master/XGS_WGS/CheckVCF.ipynb

Hope this answer your question.